I don't know how useful I can be here, but since I have a boy with very sensitive skin who almost always has something going on skin-wise, I'll try.
Ezra had thrush when he was a newborn (because I had to take antibiotics -- long, awful story), and one of the telltale signs of the yeast was the fact that the rash was across his genitals, not just his bum. It was terrible looking: red and scaly. But it didn't bother him at all-- another telltale sign of it being yeast. It also cleared up very quickly with anti-fungal cream -- very important tell-tale sign! Often, now, he gets little pimply looking bumps around his bum. They are pus-filled like you describe, but much smaller. I was told these are yeast-related, and whenever they show up, I slather on the Lotrimin.
As for the little red bumps, it sounds like either a contact dermititis, allergy or sensitivity, or chafing. WHen Ezra gets stuff like that it's usually chafing. If lotions work, chafing would make sense. So, though, could dry skin. As with most things, if he's his usual self and there's no fever or discomfort, I would wait and watch. Chances are, it will just go away entirely and you'll never really know what it was.
And keeping a food diary sounds like a good idea for him too. But, remember, just because he has a mild reaction to a food, it doesn't mean he has an allergy. More likely, it's a temporary sensitivity, and you can try the food again later.